nipype.interfaces.nipy.preprocess module¶
ComputeMask¶
Bases: NipyBaseInterface
- Mandatory Inputs:
mean_volume (a pathlike object or string representing an existing file) – Mean EPI image, used to compute the threshold for the mask.
- Optional Inputs:
M (a float) – Upper fraction of the histogram to be discarded.
cc (a boolean) – Keep only the largest connected component.
m (a float) – Lower fraction of the histogram to be discarded.
reference_volume (a pathlike object or string representing an existing file) – Reference volume used to compute the mask. If none is give, the mean volume is used.
- Outputs:
brain_mask (a pathlike object or string representing an existing file)
SpaceTimeRealigner¶
Bases: NipyBaseInterface
Simultaneous motion and slice timing correction algorithm
If slice_times is not specified, this algorithm performs spatial motion correction
This interface wraps nipy’s SpaceTimeRealign algorithm [Roche2011] or simply the SpatialRealign algorithm when timing info is not provided.
Examples
>>> from nipype.interfaces.nipy import SpaceTimeRealigner >>> #Run spatial realignment only >>> realigner = SpaceTimeRealigner() >>> realigner.inputs.in_file = ['functional.nii'] >>> res = realigner.run()>>> realigner = SpaceTimeRealigner() >>> realigner.inputs.in_file = ['functional.nii'] >>> realigner.inputs.tr = 2 >>> realigner.inputs.slice_times = list(range(0, 3, 67)) >>> realigner.inputs.slice_info = 2 >>> res = realigner.run()References
- Mandatory Inputs:
in_file (a list of items which are a pathlike object or string representing an existing file) – File to realign.
- Optional Inputs:
slice_info (an integer or a list of items which are any value) – Single integer or length 2 sequence If int, the axis in images that is the slice axis. In a 4D image, this will often be axis = 2. If a 2 sequence, then elements are
(slice_axis, slice_direction)
, whereslice_axis
is the slice axis in the image as above, andslice_direction
is 1 if the slices were acquired slice 0 first, slice -1 last, or -1 if acquired slice -1 first, slice 0 last. If slice_info is an int, assumeslice_direction
== 1. Requires inputs:slice_times
.slice_times (a list of items which are a float or ‘asc_alt_2’ or ‘asc_alt_2_1’ or ‘asc_alt_half’ or ‘asc_alt_siemens’ or ‘ascending’ or ‘desc_alt_2’ or ‘desc_alt_half’ or ‘descending’) – Actual slice acquisition times.
tr (a float) – TR in seconds. Requires inputs:
slice_times
.- Outputs:
out_file (a list of items which are a pathlike object or string representing an existing file) – Realigned files.
par_file (a list of items which are a pathlike object or string representing an existing file) – Motion parameter files. Angles are not euler angles.
- SpaceTimeRealigner.keywords = ['slice timing', 'motion correction']¶
Trim¶
Bases: NipyBaseInterface
Simple interface to trim a few volumes from a 4d fmri nifti file
Examples
>>> from nipype.interfaces.nipy.preprocess import Trim >>> trim = Trim() >>> trim.inputs.in_file = 'functional.nii' >>> trim.inputs.begin_index = 3 # remove 3 first volumes >>> res = trim.run()
- Mandatory Inputs:
in_file (a pathlike object or string representing an existing file) – EPI image to trim.
- Optional Inputs:
begin_index (an integer) – First volume. (Nipype default value:
0
)end_index (an integer) – Last volume indexed as in python (and 0 for last). (Nipype default value:
0
)out_file (a pathlike object or string representing a file) – Output filename.
suffix (a string) – Suffix for out_file to use if no out_file provided. (Nipype default value:
_trim
)- Outputs:
out_file (a pathlike object or string representing an existing file)